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Nome                                                   Pier Federico Gherardini

Data e luogo di nascita                  Roma, 12 / 8 / 1982

Indirizzo di residenza                     Via Ridolfino Venuti 26, 00162, Roma, Italia

 

Nazionalità                                         Italiana

 

Lingue parlate                                   Italiano (lingua materna)

                                                                Inglese (livello C2)

 

Numero ORCID                                0000-0002-9030-2154

 

Posizione attuale

Professore Associato di Biologia Molecolare (BIO/11)

 

Formazione

2004

Laurea triennale in biotecnologie cum laude –

Università di Tor Vergata, Roma, Italia

2006

Laurea specialistica in bioinformatica cum laude –

Università di Tor Vergata, Roma, Italia

2009

Dottorato in Biologia Cellulare e Molecolare –

Università di Tor Vergata, Roma, Italia

2016

Ignite Certificate Program in Innovation and Entrepreneurship – Stanford Graduate School of Business, Stanford, CA, USA

2020

Developing Executive Leadership training certificate –

American Management Association

                                               

 

Premi e distinzioni

2007

Premio “Sebastiano e Rita Raeli” per i migliori laureati dell’Università di Roma, Tor Vergata

2013

Human Frontier Science Program Postdoctoral Fellowship (rifiutata)

2013

Life Sciences Research Foundation Postdoctoral Fellowship

 

 

 

 

 

 

 

 

 

Precedenti posizioni

Set 2005 – Nov 2005

Visiting scientist presso il laboratorio del Prof. Michael JE Sternberg – Imperial College, London, UK

Gen 2010 – Ott 2012

Ricercatore post-doc presso il laboratorio della Prof.ssa Manuela Helmer-Citterich – Università di Tor Vergata, Roma, Italia

Ott 2012 – Ago 2016

Ricercatore post-doc presso il laboratorio del prof. Garry Nolan – Stanford University Medical School, Stanford, CA, USA

Nov 2015

Co-fondatore di HepaTx corporation – Palo Alto, CA, USA

Set 2016 – Gen 2018

Senior scientist presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

Gen 2018 – Gen 2019

Associate Director of Technology Development presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

Gen 2019 – Feb 2021

Director of Informatics presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

 

Insegnamento

2004 – 2005

2005 – 2006

2006 – 2007

2007 – 2008

Assistente per le esercitazioni pratiche e membro nelle Commissioni di esame per il corso di Bioinformatica (4 cfu) SSD BIO/11 nella LT in Biologia Cellulare e Molecolare – Università di Tor Vergata, Roma, Italia

2004 – 2005

2005 – 2006

2006 – 2007

2007 – 2008

Assistente per le esercitazioni pratiche e membro nelle Commissioni di esame per il corso di Bioinformatica Molecolare (4 cfu) SSD BIO/11 nella LM in Biologia Cellulare e Molecolare – Università di Tor Vergata, Roma, Italia

2009 – 2010

2010 – 2011

2011 – 2012

Docente del modulo “Algoritmi della Bioinformatica” (2 cfu) SSD BIO/11 nel Corso Integrato “Applicazioni web per la Biomedicina e Algoritmi della Bioinformatica”, curriculare nella LM Bioinformatica – Università di Tor Vergata, Roma, Italia

2016

Assistente per il corso BIO 150 Human Behavioral Biology – Stanford University, Stanford, CA, USA

2014 - 2018

Docente per il workshop Stanford phosphoflow Immune Monitoring Course – Stanford University, Stanford, CA, USA

Set 2017

Docente per il workshop Inserm Workshop 247. Flow, mass, spectral cytometry and analysis tools for multiparametric data analysis – Bordeaux, Francia

Mar 2019

Docente per il corso NCGR/NM-INBRE Integrative Omics workshop – Santa Fe, NM, USA

Feb 2021

Docente per il corso SITC (Society for Immunotherapy of Cancer) Winter school – San Francisco, CA, USA

 

2023 – 2024

Titolare del Corso di Espressione Genica (6 cfu) nella LM in Biologia Cellulare e Molecolare e Scienze Biologiche – Universita’ di Roma Tor Vergata

2024 – 2025

Titolare del Corso di Bioinformatica(6 cfu) nella LM in Bioinformatica -  Universita’ di Roma Tor Vergata

 

Supervisione di studenti

2006 - 2009

Iolanda Mangone

Studente di Dottorato

2006 - 2009

Antonio Palmeri

Studente di Dottorato

2006 - 2009

Luca Parca

Studente di Dottorato

2006 - 2009

Valerio Bianchi

Studente di Dottorato

 

 

Interessi scientifici  

 

 

Presentazioni orali a congressi internazionali

2008

Bioinformatics Italian Society (BITS) Meeting – Rome, Italy

2010

Leishdrug (FP7 EU) project mid-term meeting – Paris, France

2012

Leishdrug (FP7 EU) project final meeting – Paris, France

2012

Bioinformatics Italian Society (BITS) Meeting – Catania, Italy

2015

International Conference on Systems Biology of Human Disease – Heidelberg, Germany

2015

CYTO – Glasgow, UK

2016

CYTO – Seattle, WA, USA

2016

International Society for Stem Cell Research – San Francisco, CA, USA

2019

Clojure Conj – Durham, NC, USA

 

 

Presentazioni su invito a congressi internazionali

2018

CZI Analysis of Multimodal Cohort Datasets workshop – San Francisco, CA, USA

2018

Immuno-Oncology Biomarkers: State of the art – San Francisco, CA, USA

2019

The III Siena Think Tank “A Vision of I-O: call for actions” – Siena, Italy

2019

American Association for Precision Medicine Annual Meeting – Santa Clara, CA, USA

2020

ITOC7 7th Immunotherapy of Cancer Conference – Vienna, Austria

2021

Festival of Biologics USA: World Immunotherapy Congress 2021 – San Francisco, CA, USA

 

 

Pubblicazioni e attività editoriali

48 Articoli pubblicati in riviste scientifiche internazionali (h-index = 29):

 

  1. Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Artificial intelligence methods enhance the discovery of RNA interactions. Front Mol Biosci. 2022 Oct 7;9:1000205. doi: 10.3389/fmolb.2022.1000205. PMID: 36275611; PMCID: PMC9585310.
  2. Padrón LJ, Maurer DM, O'Hara MH, O'Reilly EM, Wolff RA, Wainberg ZA, Ko AH, Fisher G, Rahma O, Lyman JP, Cabanski CR, Yu JX, Pfeiffer SM, Spasic M, Xu J, Gherardini PF, Karakunnel J, Mick R, Alanio C, Byrne KT, Hollmann TJ, Moore JS, Jones DD, Tognetti M, Chen RO, Yang X, Salvador L, Wherry EJ, Dugan U, O'Donnell-Tormey J, Butterfield LH, Hubbard-Lucey VM, Ibrahim R, Fairchild J, Bucktrout S, LaVallee TM, Vonderheide RH. Sotigalimab and/or nivolumab with chemotherapy in first-line metastatic pancreatic cancer: clinical and immunologic analyses from the randomized phase 2 PRINCE trial. Nat Med. 2022 Jun;28(6):1167-1177. doi: 10.1038/s41591-022-01829-9. Epub 2022 Jun 3. PMID: 35662283; PMCID: PMC9205784.
  3. Chan V, Gherardini PF, Krummel MF, Fragiadakis GK. A "data sharing trust" model for rapid, collaborative science. Cell. 2021 Feb 4;184(3):566-570.
  4. Friedman CF, Spencer C, Cabanski CR, Panageas KS, Wells DK, Ribas A, Tawbi H, Tsai K, Postow M, Shoushtari A, Chapman P, Karakunnel J, Bucktrout S, Gherardini P, Hollmann TJ, Chen RO, Callahan M, LaVallee T, Ibrahim R, Wolchok J. Ipilimumab alone or in combination with nivolumab in patients with advanced melanoma who have progressed or relapsed on PD-1 blockade: clinical outcomes and translational biomarker analyses. J Immunother Cancer. 2022 Jan;10(1):e003853. doi: 10.1136/jitc-2021-003853. PMID: 35074903; PMCID: PMC8788323.
  5. O’Hara MH, O’Reilly EM, Varadhachary G, Wolff RA, Wainberg ZA, Ko AH, Fisher G, Rahma O, Lyman JP, Cabanski CR, Mick R, Gherardini PF, Kitch L, Xu J, Samuel T, Karakunnel J, Fairchild J, Bucktrout S, LaVallee TM, Selinsky C, Till JE, Carpenter EL, Alanio C, Byrne KT, Chen RO, Trifan OC, Dugan U, Horak C, Hubbard-Lucey VM, Wherry EJ, Ibrahim R, Vonderheide RH. CD40 agonistic monoclonal antibody APX005M (sotigalimab) and chemotherapy, with or without nivolumab, for the treatment of metastatic pancreatic adenocarcinoma: an open-label, multicentre, phase 1b study. Lancet Oncol. 2021 Jan;22(1):118-131
  6. Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR: Landscape of coordinated immune responses to H1N1 challenge in humans. J Clin Invest. 2020 Nov 2;130(11):5800-5816
  7. Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC. Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell Rep. 2019 Jul 16;28(3):819-831.e4.
  8. Duckworth AD*, Gherardini PF*, Sykorova M, Yasin F, Nolan GP, Slupsky JR, Kalakonda N. Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry. Nat Protoc. 2019 Mar;14(3):901-920. *: Joint first authors
  9. Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ: MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Rep. 2018 Jul 31;24(5):1377-1388
  10. Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP: GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics. 2018 Dec 1;34(23):4131-4133
  11. Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ: Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 2018 May 15;48(5):1029-1045.e5.
  12. Eroglu Z, Zaretsky JM, Hu-Lieskovan S, Kim DW, Algazi A, Johnson DB, Liniker E, Kong B, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph R, Postow MA, Carlino MS, Hwu WJ, Scoyler RA, Messina J, Cochran AJ, Long GV, Ribas A: High response rate to PD-1 blockade in desmoplastic melanomas. Nature. 2018 Jan 18;553(7688):347-350
  13. Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG: Systemic Immunity Is Required for Effective Cancer Immunotherapy. Cell. 2017 Jan 26;168(3):487-502.e15.
  14. Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP: High-throughput precision measurement of subcellular localization in single cells. Cytometry A. 2017 Feb;91(2):180-189. doi: 10.1002/cyto.a.23054
  15. Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL: Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol. 2016 Dec 1;197(11):4482-4492.
  16. Sacco F, Silvestri A, Posca D, Pirrò S, Gherardini PF, Castagnoli L, Mann M, Cesareni G: Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State. Cell Systems. 2016 Mar 23;2(3):159–171
  17. Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen S, Nolan GP*, Gherardini PF*: Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods. 2016 Jan 25. doi: 10.1038/nmeth.3742. *: Corresponding authors
  18. Spitzer MH*, Gherardini PF*, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP: An interactive reference framework for modeling a dynamic immune system. Science. 2015 Jul 10;349(6244):1259425.   *: Joint first authors
  19. O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM: Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus. J Allergy Clin Immunol. 2015 May 30. pii: S0091-6749 (15) 00544-8
  20. Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F: AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 2015 Jan;17(1):20-30
  21. Palmeri A, Ausiello G, Ferre F, Helmer-Citterich M, Gherardini PF: A proteome-wide Domain-centric Perspective on Protein Phosphorylation. Mol Cell Proteomics. 2014 May 15. pii: mcp.M114.039990
  22. Tsigankov P, Gherardini PF, Helmer-Citterich M, Spaeth GF, Myler PJ, Zilberstein D.: Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol Cell Proteomics. 2014 April 16, doi: 10.1074/mcp.M114.037705
  23. Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F.: Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics. 2013 Jun 7;14:379
  24. Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D.: Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. J Proteome Res. 2013 Jul 5;12(7): 3405-12
  25. Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF.: Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics. 2013 Jun 28;86:97-104.
  26. Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G: Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One. 2012;7(11):e50240
  27. Gherardini PF, Helmer-Citterich M: Experimental and computational methods for the analysis and modeling of signaling networks. N Biotechnol. 2013 Mar 25;30(3):327-32
  28. Perfetto L*, Gherardini PF*, Davey NE, Diella F, Helmer-Citterich M, Cesareni G: Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci. 2013 Jan;38(1):38-46.          *: Joint first authors
  29. Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G: Mapping the human phosphatome on growth pathways. Mol Syst Biol. 2012 Aug 14;8:603
  30. Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A.: B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem. 2012;5:11-21
  31. Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G: Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S17
  32. Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D: What has proteomics taught us about Leishmania development? Parasitology 2012 Feb 28:1-12
  33. Palmeri A*, Gherardini PF*§, Tsigankov P, Ausiello G, Spath GF, Zilberstein D, Helmer-Citterich M: PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics 2011 Dec 19;12(1):614 *: Joint first authors, §: Corresponding author
  34. Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.: Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82.
  35. Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF.: Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics 2011 Aug 24;74(9):1644-51.
  36. Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G.: Phosphate binding sites identification in protein structures. Nucleic Acids Res. 2011 Mar;39(4):1231-42.
  37. Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A.: Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71.
  38. Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF. Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses. Proteomics. 2010 Nov;10(21):3868-83
  39. Gherardini PF, Ausiello G, Helmer-Citterich M.: Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One. 2010 Aug 5;5(8):e11988.
  40. Gherardini PF*, Ausiello G*, Russell RB, Helmer-Citterich M: Modular architecture of nucleotide-binding pockets. Nucleic Acids Res. 2010 Jun 1;38(11):3809-16. *: Joint first authors
  41. Ciaffi R, De Angelis D, Gherardini PF, Arcudi G, Nessi R, Cornalba GP, Grandi M, Cattaneo C: Identification from chest X-rays: reliability of bone density patterns of the humerus. J Forensic Sci. 2010 55(2): 478-481
  42. Ausiello G*, Gherardini PF*, Gatti E, Incani O, Helmer-Citterich M: Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics. 2009, 10:182. *: Joint first authors
  43. Gherardini PF, Helmer-Citterich M: Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302.
  44. Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.: FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2.
  45. Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ.: Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol. 2007 Sep 21;372(3):817-45.
  46. Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M.: 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W416-9.
  47. Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M.: False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics. 2007 Mar 1;8:68.
  48. Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M.: Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31.

 

 

 

Reviewer per: Nature Cancer, American Journal of Human Genetics, Bioinformatics, FEBS Letters, Molecular Systems Biology, Nucleic Acids Research, IEEE/ACM Transactions on Computational Biology, Journal of Proteomics, Genome Medicine

 

 

Informazioni personali

 

Nome                                                   Pier Federico Gherardini

Data e luogo di nascita                  Roma, 12 / 8 / 1982

Indirizzo di residenza                     Via Ridolfino Venuti 26, 00162, Roma, Italia

 

Nazionalità                                         Italiana

 

Lingue parlate                                   Italiano (lingua materna)

                                                                Inglese (livello C2)

 

Numero ORCID                                0000-0002-9030-2154

 

Posizione attuale

Professore Associato di Biologia Molecolare (BIO/11)

 

Formazione

2004

Laurea triennale in biotecnologie cum laude –

Università di Tor Vergata, Roma, Italia

2006

Laurea specialistica in bioinformatica cum laude –

Università di Tor Vergata, Roma, Italia

2009

Dottorato in Biologia Cellulare e Molecolare –

Università di Tor Vergata, Roma, Italia

2016

Ignite Certificate Program in Innovation and Entrepreneurship – Stanford Graduate School of Business, Stanford, CA, USA

2020

Developing Executive Leadership training certificate –

American Management Association

                                               

 

Premi e distinzioni

2007

Premio “Sebastiano e Rita Raeli” per i migliori laureati dell’Università di Roma, Tor Vergata

2013

Human Frontier Science Program Postdoctoral Fellowship (rifiutata)

2013

Life Sciences Research Foundation Postdoctoral Fellowship

 

 

 

 

 

 

 

 

 

Precedenti posizioni

Set 2005 – Nov 2005

Visiting scientist presso il laboratorio del Prof. Michael JE Sternberg – Imperial College, London, UK

Gen 2010 – Ott 2012

Ricercatore post-doc presso il laboratorio della Prof.ssa Manuela Helmer-Citterich – Università di Tor Vergata, Roma, Italia

Ott 2012 – Ago 2016

Ricercatore post-doc presso il laboratorio del prof. Garry Nolan – Stanford University Medical School, Stanford, CA, USA

Nov 2015

Co-fondatore di HepaTx corporation – Palo Alto, CA, USA

Set 2016 – Gen 2018

Senior scientist presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

Gen 2018 – Gen 2019

Associate Director of Technology Development presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

Gen 2019 – Feb 2021

Director of Informatics presso il Parker Institute for Cancer Immunotherapy – San Francisco, CA, USA

 

Insegnamento

2004 – 2005

2005 – 2006

2006 – 2007

2007 – 2008

Assistente per le esercitazioni pratiche e membro nelle Commissioni di esame per il corso di Bioinformatica (4 cfu) SSD BIO/11 nella LT in Biologia Cellulare e Molecolare – Università di Tor Vergata, Roma, Italia

2004 – 2005

2005 – 2006

2006 – 2007

2007 – 2008

Assistente per le esercitazioni pratiche e membro nelle Commissioni di esame per il corso di Bioinformatica Molecolare (4 cfu) SSD BIO/11 nella LM in Biologia Cellulare e Molecolare – Università di Tor Vergata, Roma, Italia

2009 – 2010

2010 – 2011

2011 – 2012

Docente del modulo “Algoritmi della Bioinformatica” (2 cfu) SSD BIO/11 nel Corso Integrato “Applicazioni web per la Biomedicina e Algoritmi della Bioinformatica”, curriculare nella LM Bioinformatica – Università di Tor Vergata, Roma, Italia

2016

Assistente per il corso BIO 150 Human Behavioral Biology – Stanford University, Stanford, CA, USA

2014 - 2018

Docente per il workshop Stanford phosphoflow Immune Monitoring Course – Stanford University, Stanford, CA, USA

Set 2017

Docente per il workshop Inserm Workshop 247. Flow, mass, spectral cytometry and analysis tools for multiparametric data analysis – Bordeaux, Francia

Mar 2019

Docente per il corso NCGR/NM-INBRE Integrative Omics workshop – Santa Fe, NM, USA

Feb 2021

Docente per il corso SITC (Society for Immunotherapy of Cancer) Winter school – San Francisco, CA, USA

 

2023 – 2024

Titolare del Corso di Espressione Genica (6 cfu) nella LM in Biologia Cellulare e Molecolare e Scienze Biologiche – Universita’ di Roma Tor Vergata

2024 – 2025

Titolare del Corso di Bioinformatica(6 cfu) nella LM in Bioinformatica -  Universita’ di Roma Tor Vergata

 

Supervisione di studenti

2006 - 2009

Iolanda Mangone

Studente di Dottorato

2006 - 2009

Antonio Palmeri

Studente di Dottorato

2006 - 2009

Luca Parca

Studente di Dottorato

2006 - 2009

Valerio Bianchi

Studente di Dottorato

 

 

Interessi scientifici  

 

 

Presentazioni orali a congressi internazionali

2008

Bioinformatics Italian Society (BITS) Meeting – Rome, Italy

2010

Leishdrug (FP7 EU) project mid-term meeting – Paris, France

2012

Leishdrug (FP7 EU) project final meeting – Paris, France

2012

Bioinformatics Italian Society (BITS) Meeting – Catania, Italy

2015

International Conference on Systems Biology of Human Disease – Heidelberg, Germany

2015

CYTO – Glasgow, UK

2016

CYTO – Seattle, WA, USA

2016

International Society for Stem Cell Research – San Francisco, CA, USA

2019

Clojure Conj – Durham, NC, USA

 

 

Presentazioni su invito a congressi internazionali

2018

CZI Analysis of Multimodal Cohort Datasets workshop – San Francisco, CA, USA

2018

Immuno-Oncology Biomarkers: State of the art – San Francisco, CA, USA

2019

The III Siena Think Tank “A Vision of I-O: call for actions” – Siena, Italy

2019

American Association for Precision Medicine Annual Meeting – Santa Clara, CA, USA

2020

ITOC7 7th Immunotherapy of Cancer Conference – Vienna, Austria

2021

Festival of Biologics USA: World Immunotherapy Congress 2021 – San Francisco, CA, USA

 

 

Pubblicazioni e attività editoriali

48 Articoli pubblicati in riviste scientifiche internazionali (h-index = 29):

 

  1. Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Artificial intelligence methods enhance the discovery of RNA interactions. Front Mol Biosci. 2022 Oct 7;9:1000205. doi: 10.3389/fmolb.2022.1000205. PMID: 36275611; PMCID: PMC9585310.
  2. Padrón LJ, Maurer DM, O'Hara MH, O'Reilly EM, Wolff RA, Wainberg ZA, Ko AH, Fisher G, Rahma O, Lyman JP, Cabanski CR, Yu JX, Pfeiffer SM, Spasic M, Xu J, Gherardini PF, Karakunnel J, Mick R, Alanio C, Byrne KT, Hollmann TJ, Moore JS, Jones DD, Tognetti M, Chen RO, Yang X, Salvador L, Wherry EJ, Dugan U, O'Donnell-Tormey J, Butterfield LH, Hubbard-Lucey VM, Ibrahim R, Fairchild J, Bucktrout S, LaVallee TM, Vonderheide RH. Sotigalimab and/or nivolumab with chemotherapy in first-line metastatic pancreatic cancer: clinical and immunologic analyses from the randomized phase 2 PRINCE trial. Nat Med. 2022 Jun;28(6):1167-1177. doi: 10.1038/s41591-022-01829-9. Epub 2022 Jun 3. PMID: 35662283; PMCID: PMC9205784.
  3. Chan V, Gherardini PF, Krummel MF, Fragiadakis GK. A "data sharing trust" model for rapid, collaborative science. Cell. 2021 Feb 4;184(3):566-570.
  4. Friedman CF, Spencer C, Cabanski CR, Panageas KS, Wells DK, Ribas A, Tawbi H, Tsai K, Postow M, Shoushtari A, Chapman P, Karakunnel J, Bucktrout S, Gherardini P, Hollmann TJ, Chen RO, Callahan M, LaVallee T, Ibrahim R, Wolchok J. Ipilimumab alone or in combination with nivolumab in patients with advanced melanoma who have progressed or relapsed on PD-1 blockade: clinical outcomes and translational biomarker analyses. J Immunother Cancer. 2022 Jan;10(1):e003853. doi: 10.1136/jitc-2021-003853. PMID: 35074903; PMCID: PMC8788323.
  5. O’Hara MH, O’Reilly EM, Varadhachary G, Wolff RA, Wainberg ZA, Ko AH, Fisher G, Rahma O, Lyman JP, Cabanski CR, Mick R, Gherardini PF, Kitch L, Xu J, Samuel T, Karakunnel J, Fairchild J, Bucktrout S, LaVallee TM, Selinsky C, Till JE, Carpenter EL, Alanio C, Byrne KT, Chen RO, Trifan OC, Dugan U, Horak C, Hubbard-Lucey VM, Wherry EJ, Ibrahim R, Vonderheide RH. CD40 agonistic monoclonal antibody APX005M (sotigalimab) and chemotherapy, with or without nivolumab, for the treatment of metastatic pancreatic adenocarcinoma: an open-label, multicentre, phase 1b study. Lancet Oncol. 2021 Jan;22(1):118-131
  6. Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR: Landscape of coordinated immune responses to H1N1 challenge in humans. J Clin Invest. 2020 Nov 2;130(11):5800-5816
  7. Hartmann FJ, Babdor J, Gherardini PF, Amir ED, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC. Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell Rep. 2019 Jul 16;28(3):819-831.e4.
  8. Duckworth AD*, Gherardini PF*, Sykorova M, Yasin F, Nolan GP, Slupsky JR, Kalakonda N. Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry. Nat Protoc. 2019 Mar;14(3):901-920. *: Joint first authors
  9. Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ: MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Rep. 2018 Jul 31;24(5):1377-1388
  10. Aghaeepour N, Simonds EF, Knapp DJHF, Bruggner RV, Sachs K, Culos A, Gherardini PF, Samusik N, Fragiadakis GK, Bendall SC, Gaudilliere B, Angst MS, Eaves CJ, Weiss WA, Fantl WJ, Nolan GP: GateFinder: projection-based gating strategy optimization for flow and mass cytometry. Bioinformatics. 2018 Dec 1;34(23):4131-4133
  11. Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ: Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 2018 May 15;48(5):1029-1045.e5.
  12. Eroglu Z, Zaretsky JM, Hu-Lieskovan S, Kim DW, Algazi A, Johnson DB, Liniker E, Kong B, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph R, Postow MA, Carlino MS, Hwu WJ, Scoyler RA, Messina J, Cochran AJ, Long GV, Ribas A: High response rate to PD-1 blockade in desmoplastic melanomas. Nature. 2018 Jan 18;553(7688):347-350
  13. Spitzer MH, Carmi Y, Reticker-Flynn NE, Kwek SS, Madhireddy D, Martins MM, Gherardini PF, Prestwood TR, Chabon J, Bendall SC, Fong L, Nolan GP, Engleman EG: Systemic Immunity Is Required for Effective Cancer Immunotherapy. Cell. 2017 Jan 26;168(3):487-502.e15.
  14. Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP: High-throughput precision measurement of subcellular localization in single cells. Cytometry A. 2017 Feb;91(2):180-189. doi: 10.1002/cyto.a.23054
  15. Fragiadakis GK, Baca QJ, Gherardini PF, Ganio EA, Gaudilliere DK, Tingle M, Lancero HL, McNeil LS, Spitzer MH, Wong RJ, Shaw GM, Darmstadt GL, Sylvester KG, Winn VD, Carvalho B, Lewis DB, Stevenson DK, Nolan GP, Aghaeepour N, Angst MS, Gaudilliere BL: Mapping the Fetomaternal Peripheral Immune System at Term Pregnancy. J Immunol. 2016 Dec 1;197(11):4482-4492.
  16. Sacco F, Silvestri A, Posca D, Pirrò S, Gherardini PF, Castagnoli L, Mann M, Cesareni G: Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State. Cell Systems. 2016 Mar 23;2(3):159–171
  17. Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen S, Nolan GP*, Gherardini PF*: Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods. 2016 Jan 25. doi: 10.1038/nmeth.3742. *: Corresponding authors
  18. Spitzer MH*, Gherardini PF*, Fragiadakis GK, Bhattacharya N, Yuan RT, Hotson AN, Finck R, Carmi Y, Zunder ER, Fantl WJ, Bendall SC, Engleman EG, Nolan GP: An interactive reference framework for modeling a dynamic immune system. Science. 2015 Jul 10;349(6244):1259425.   *: Joint first authors
  19. O'Gorman WE, Hsieh EW, Savig ES, Gherardini PF, Hernandez JD, Hansmann L, Balboni IM, Utz PJ, Bendall SC, Fantl WJ, Lewis DB, Nolan GP, Davis MM: Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus. J Allergy Clin Immunol. 2015 May 30. pii: S0091-6749 (15) 00544-8
  20. Cianfanelli V, Fuoco C, Lorente M, Salazar M, Quondamatteo F, Gherardini PF, De Zio D, Nazio F, Antonioli M, D'Orazio M, Skobo T, Bordi M, Rohde M, Dalla Valle L, Helmer-Citterich M, Gretzmeier C, Dengjel J, Fimia GM, Piacentini M, Di Bartolomeo S, Velasco G, Cecconi F: AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol. 2015 Jan;17(1):20-30
  21. Palmeri A, Ausiello G, Ferre F, Helmer-Citterich M, Gherardini PF: A proteome-wide Domain-centric Perspective on Protein Phosphorylation. Mol Cell Proteomics. 2014 May 15. pii: mcp.M114.039990
  22. Tsigankov P, Gherardini PF, Helmer-Citterich M, Spaeth GF, Myler PJ, Zilberstein D.: Regulation dynamics of Leishmania differentiation: deconvoluting signals and identifying phosphorylation trends. Mol Cell Proteomics. 2014 April 16, doi: 10.1074/mcp.M114.037705
  23. Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F.: Alternative splicing tends to avoid partial removals of protein-protein interaction sites. BMC Genomics. 2013 Jun 7;14:379
  24. Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D.: Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. J Proteome Res. 2013 Jul 5;12(7): 3405-12
  25. Leclercq O, Bartho K, Duelsner E, von Kleist L, Gherardini PF, Palmeri A, Helmer-Citterich M, Baumgart S, Späth GF.: Enrichment of Leishmania donovani ATP-binding proteins using a staurosporine capture compound. J Proteomics. 2013 Jun 28;86:97-104.
  26. Parca L, Gherardini PF, Truglio M, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G: Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One. 2012;7(11):e50240
  27. Gherardini PF, Helmer-Citterich M: Experimental and computational methods for the analysis and modeling of signaling networks. N Biotechnol. 2013 Mar 25;30(3):327-32
  28. Perfetto L*, Gherardini PF*, Davey NE, Diella F, Helmer-Citterich M, Cesareni G: Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci. 2013 Jan;38(1):38-46.          *: Joint first authors
  29. Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G: Mapping the human phosphatome on growth pathways. Mol Syst Biol. 2012 Aug 14;8:603
  30. Giacò L, Amicosante M, Fraziano M, Gherardini PF, Ausiello G, Helmer-Citterich M, Colizzi V, Cabibbo A.: B-Pred, a structure based B-cell epitopes prediction server. Adv Appl Bioinform Chem. 2012;5:11-21
  31. Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G: Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S17
  32. Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D: What has proteomics taught us about Leishmania development? Parasitology 2012 Feb 28:1-12
  33. Palmeri A*, Gherardini PF*§, Tsigankov P, Ausiello G, Spath GF, Zilberstein D, Helmer-Citterich M: PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics 2011 Dec 19;12(1):614 *: Joint first authors, §: Corresponding author
  34. Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M.: Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W278-82.
  35. Schmidt-Arras D, Leclercq O, Gherardini PF, Helmer-Citterich M, Faigle W, Loew D, Späth GF.: Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics 2011 Aug 24;74(9):1644-51.
  36. Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G.: Phosphate binding sites identification in protein structures. Nucleic Acids Res. 2011 Mar;39(4):1231-42.
  37. Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A.: Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71.
  38. Hem S, Gherardini PF, Osorio y Fortéa J, Hourdel V, Morales MA, Watanabe R, Pescher P, Kuzyk MA, Smith D, Borchers CH, Zilberstein D, Helmer-Citterich M, Namane A, Späth GF. Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses. Proteomics. 2010 Nov;10(21):3868-83
  39. Gherardini PF, Ausiello G, Helmer-Citterich M.: Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One. 2010 Aug 5;5(8):e11988.
  40. Gherardini PF*, Ausiello G*, Russell RB, Helmer-Citterich M: Modular architecture of nucleotide-binding pockets. Nucleic Acids Res. 2010 Jun 1;38(11):3809-16. *: Joint first authors
  41. Ciaffi R, De Angelis D, Gherardini PF, Arcudi G, Nessi R, Cornalba GP, Grandi M, Cattaneo C: Identification from chest X-rays: reliability of bone density patterns of the humerus. J Forensic Sci. 2010 55(2): 478-481
  42. Ausiello G*, Gherardini PF*, Gatti E, Incani O, Helmer-Citterich M: Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics. 2009, 10:182. *: Joint first authors
  43. Gherardini PF, Helmer-Citterich M: Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302.
  44. Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.: FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2.
  45. Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ.: Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol. 2007 Sep 21;372(3):817-45.
  46. Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M.: 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W416-9.
  47. Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M.: False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics. 2007 Mar 1;8:68.
  48. Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M.: Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31.

 

 

 

Reviewer per: Nature Cancer, American Journal of Human Genetics, Bioinformatics, FEBS Letters, Molecular Systems Biology, Nucleic Acids Research, IEEE/ACM Transactions on Computational Biology, Journal of Proteomics, Genome Medicine

 

 

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